Mapping of 228 ESTs and 26 Genes into an Integrated Physical and Genetic Map of Human Chromosome 17
ABSTRACT We have integrated genetic and physical mapping data for chromosome 17 subdivided into 26 bins, by using a panel of chromosome 17 deletion somatic cell hybrids. One hundred four short tandem repeat and STS markers have been localized into these bins and have enabled the ordering of 288 ESTs and 26 genes, including 142 ESTs that had not been previously sublocalized on chromosome 17. The mapping information of several genetic maps, as well as information obtained by radiation hybrid and STS content mapping of YACs, has been integrated using this hybrid panel. Although existing mapping information for chromosome 17 was generally consistent for many ESTs previously mapped, the map presented here further refines the location of ESTs, as well as demonstrating a number of discrepancies found in the 17q24-q25 region. We attribute these discrepancies to the fact that the current radiation hybrid panels were selected for retention of the thymidine kinase gene at 17q25, as well as to a low concentration of YAC contigs in this region. These data illustrate the benefit of combining multiple mapping techniques to obtain the greatest accuracy. The integration of maps developed by different methods will generate the most accurate genome maps, which may then be used for the generation of large insert clone contigs for chromosome sequencing. Additionally, accurate transcript maps generated by ESTs will greatly speed the isolation of genes linked to disease loci.
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- "The vast majority of the clones were selected from human chromosome 17 database resources, such as the Sanger Institute and the Weizmann Institute, as well as genome resources, such as the National Center for Biotechnology Information (NCBI), for their content of STSs, ESTs, or genes described previously in the 17p13.3 region (Stack et al. 1995; Plummer et al. 1997; Hoff et al. 2000; McHale et al. 2000). All genomic clones were purchased from Research Genetics. "
ABSTRACT: Deletions of 17p13.3, including the LIS1 gene, result in the brain malformation lissencephaly, which is characterized by reduced gyration and cortical thickening; however, the phenotype can vary from isolated lissencephaly sequence (ILS) to Miller-Dieker syndrome (MDS). At the clinical level, these two phenotypes can be differentiated by the presence of significant dysmorphic facial features and a more severe grade of lissencephaly in MDS. Previous work has suggested that children with MDS have a larger deletion than those with ILS, but the precise boundaries of the MDS critical region and causative genes other than LIS1 have never been fully determined. We have completed a physical and transcriptional map of the 17p13.3 region from LIS1 to the telomere. Using fluorescence in situ hybridization, we have mapped the deletion size in 19 children with ILS, 11 children with MDS, and 4 children with 17p13.3 deletions not involving LIS1. We show that the critical region that differentiates ILS from MDS at the molecular level can be reduced to 400 kb. Using somatic cell hybrids from selected patients, we have identified eight genes that are consistently deleted in patients classified as having MDS. In addition, deletion of the genes CRK and 14-3-3 epsilon delineates patients with the most severe lissencephaly grade. On the basis of recent functional data and the creation of a mouse model suggesting a role for 14-3-3 epsilon in cortical development, we suggest that deletion of one or both of these genes in combination with deletion of LIS1 may contribute to the more severe form of lissencephaly seen only in patients with MDS.The American Journal of Human Genetics 05/2003; 72(4):918-30. DOI:10.1086/374320 · 10.99 Impact Factor
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ABSTRACT: Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by an abnormal susceptibility to infection with a specific group of related human papillomavirus (HPV) genotypes, including the oncogenic HPV5 associated with the skin carcinomas developing in about half of EV patients. EV is usually considered as an autosomal recessive condition. Taking EV as a model to identify a locus underlying the susceptibility to HPV infections, we performed a genome-wide search for linkage with 255 microsatellite genetic markers in three consanguineous EV families comprising six patients, using the homozygosity mapping approach. Homozygosity restricted to affected individuals was observed for a marker of chromosome 17q (D17S784) in two families and a marker about 17 centiMorgan (cM) distal (D17S1807) in the third family. Ten additional microsatellite markers spanning 29 cM in this region were analyzed. Two-point lod score values greater than 3 were obtained for four markers and multipoint linkage analysis yielded a maximum lod score of 10.17 between markers D17S939 and D17S802. Recombination events observed in two families allowed a candidate region for the EV susceptibility locus to be mapped to the 1 cM region defined by these two markers. The EV locus (named EV1) is included in the 17qter region recently found to contain a dominant locus for the susceptibility to familial psoriasis. It has been shown that patients suffering from psoriasis are likely to constitute the reservoir of HPV5. It is thus tempting to speculate that distinct defects affecting the same gene may be involved in the two skin conditions.Journal of Investigative Dermatology 04/1999; 112(3):259-63. DOI:10.1046/j.1523-1747.1999.00536.x · 6.37 Impact Factor
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ABSTRACT: An isochromosome of the long arm of chromosome 17, i(17q), is the most frequent genetic abnormality observed during the disease progression of Philadelphia chromosome-positive chronic myeloid leukemia (CML), and has been described as the sole anomaly in various other hematologic malignancies. The i(17q) hence plays a presumably important pathogenetic role both in leukemia development and progression. This notwithstanding, the molecular consequences of this abnormality have not been investigated in detail. We have analyzed 21 hematologic malignancies (8 CML in blast crisis, 8 myelodysplastic syndromes [MDS], 2 acute myeloid leukemias, 2 chronic lymphocytic leukemias, and 1 acute lymphoblastic leukemia) with i(17q) by fluorescence in situ hybridization (FISH). Using a yeast artificial chromosome (YAC) contig, derived from the short arm of chromosome 17, all cases were shown to have a breakpoint in 17p. In 12 cases, the breaks occurred within the Smith-Magenis Syndrome (SMS) common deletion region in 17p11, a gene-rich region which is genetically unstable. In 10 of these 12 cases, we were able to further map the breakpoints to specific markers localized within a single YAC clone. Six other cases showed breakpoints located proximally to the SMS common deletion region, but still within 17p11, and yet another case had a breakpoint distal to this region. Furthermore, using chromosome 17 centromere-specific probes, it could be shown that the majority of the i(17q) chromosomes (11 of 15 investigated cases) were dicentric, ie, they contained two centromeres, strongly suggesting that i(17q) is formed through an intrachromosomal recombination event, and also implicating that the i(17q), in a formal sense, should be designated idic(17)(p11). Because i(17q) formation results in loss of 17p material, potentially uncovering the effect of a tumor suppressor on the remaining 17p, the occurrence of TP53 mutations was studied in 17 cases by sequencing the entire coding region. In 16 cases, no TP53 mutations were found, whereas one MDS displayed a homozygous deletion of TP53. Thus, our data suggest that there is no association between i(17q) and coding TP53 mutations, and that another tumor suppressor gene(s), located in proximity of the SMS common deletion region, or in a more distal location, is of pathogenetic importance in i(17q)-associated leukemia.Blood 08/1999; 94(1):225-32. · 10.43 Impact Factor